Contacts of the strand formed by residues 150 - 157 (chain A) in PDB entry 1WD5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.1 38.8 + - - +
21A GLY 4.6 4.9 + - - -
22A LEU* 3.8 26.4 - - + +
121A ARG 3.6 2.3 + - - +
122A ASP* 3.5 16.8 + - - +
123A VAL* 2.8 27.6 + - - +
148A PRO* 3.3 1.2 - - - +
149A ARG* 1.3 85.0 - - + +
151A VAL* 1.3 76.0 + - - +
152A VAL* 3.8 10.8 - - + +
171A GLU* 2.9 31.7 + - - -
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 3.3 8.5 - - + +
125A LEU* 4.2 13.5 - - + -
140A LEU* 3.7 29.6 - - + -
143A VAL* 4.3 10.5 - - + -
144A PHE* 3.6 28.0 - - + -
148A PRO* 3.4 29.4 - - + +
150A ARG* 1.3 82.5 - - - +
152A VAL* 1.3 74.0 + - - +
170A ALA* 4.3 4.6 - - + +
171A GLU* 4.2 15.1 + - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.1 13.9 - - + -
20A LEU* 4.2 4.5 - - + -
22A LEU* 4.3 15.3 - - + -
123A VAL 2.9 9.3 + - - +
124A VAL* 3.3 10.7 - - + +
125A LEU* 2.8 26.5 + - - +
150A ARG* 3.8 25.6 - - + +
151A VAL* 1.3 82.2 - - - +
153A VAL* 1.3 75.4 + - - +
154A ALA* 3.7 1.0 + - + -
171A GLU* 3.7 21.3 - - - +
173A VAL* 3.9 22.0 - - + -
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 3.6 5.6 - - + -
136A MSE 4.1 33.7 - - + -
140A LEU* 3.9 38.4 - - + -
152A VAL* 1.3 74.8 - - - +
154A ALA* 1.3 55.3 + - - +
155A VAL* 4.3 9.9 - - + -
166A LEU* 4.1 15.7 - - + -
170A ALA* 4.4 5.8 - - + -
171A GLU 2.9 15.2 + - - +
172A VAL* 3.3 15.1 - - + -
173A VAL* 2.7 33.6 + - - +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.8 19.7 - - + -
17A LEU* 3.9 29.8 - - + -
124A VAL* 3.9 17.0 - - + -
125A LEU 2.8 18.3 + - - +
126A VAL* 3.3 17.3 - - + +
152A VAL 3.7 0.4 + - - -
153A VAL* 1.3 75.2 - - - +
155A VAL* 1.3 67.4 + - - +
173A VAL 3.2 6.3 - - - +
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.9 6.9 - - - +
127A ASP 4.1 8.5 - - - +
129A GLY* 4.9 0.7 - - - -
130A VAL* 3.4 28.7 - - + -
136A MSE 4.1 16.6 - - + -
153A VAL* 4.3 7.4 - - + -
154A ALA* 1.3 79.4 - - - +
156A PRO* 1.3 70.7 - - + +
157A VAL 4.1 5.6 - - - +
158A ALA* 4.0 20.6 - - + -
166A LEU* 6.1 1.1 - - + -
172A VAL* 5.2 6.3 - - + -
173A VAL 2.9 10.0 + - - +
174A ALA* 3.2 20.8 - - + -
175A LEU 3.2 17.5 + - - -
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Residues in contact with PRO 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PHE* 3.7 23.8 - - + -
9A ALA* 3.7 17.3 - - + +
13A LEU* 4.1 9.2 - - + -
37A VAL* 4.2 13.0 - - + -
127A ASP 3.1 20.6 - - - +
128A ASP 3.7 7.0 - - - +
155A VAL* 1.3 84.4 - - + +
157A VAL* 1.3 58.6 + - - +
175A LEU* 3.2 20.9 - - + +
176A SER* 3.1 21.5 + - - -
188A TYR* 3.4 26.0 - - - +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PHE* 4.5 8.7 - - + -
128A ASP 4.1 5.8 - - - +
129A GLY* 3.4 15.0 - - - -
130A VAL 3.0 19.4 + - - -
155A VAL* 3.4 5.2 - - - +
156A PRO* 1.3 80.8 - - + +
158A ALA* 1.3 66.6 + - - +
176A SER* 3.3 18.6 - - - +
178A PRO* 3.7 20.9 - - + -
181A PHE* 4.1 9.6 - - + -
184A VAL* 4.6 7.6 - - + +
187A TYR* 4.0 37.7 - - + -
188A TYR* 4.8 3.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il